Search results for: molecular individualism

Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Richa Mardianingrum, Srie R. N. Endah

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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin

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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².

Keywords: chromophore, organic solar cells, photoactive materials, small molecule

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran (AP) and benzimidazole (BI) derivatives on J55 steel in 3.5% NaCl solution saturated with CO₂ was investigated by electrochemical, weight loss, surface characterization, and theoretical studies. The electrochemical studies included electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), electrochemical frequency modulation (EFM), and electrochemical frequency modulation trend (EFMT). Surface characterization was done using contact angle, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. DFT and molecular dynamics (MD) studies were done using Gaussian and Materials Studio softwares. All the studies suggested the good inhibition by the synthesized inhibitors on J55 steel in 3.5% NaCl solution saturated with CO₂ due to the formation of a protective film on the surface. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface.

Keywords: corrosion, inhibitor, EFM, AFM, DFT, MD

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Authors: Majid Farsadrooh, Mehran Feizi-Dehnayebi

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Serum albumin is the most abundant protein that is present in the circulatory system of a wide variety of organisms. Although it is a significant macromolecule, it can contribute to osmotic blood pressure and also, plays a superior role in drug disposition and efficiency. Molecular docking simulation can improve in silico drug design and discovery procedures to propound a lead compound and develop it from the discovery step to the clinic. In this study, the molecular docking simulation was applied to select a lead molecule through an investigation of the interaction of the two anticancer drugs (Alitretinoin and Abemaciclib) with Human Serum Albumin (HSA). Then, a series of new compounds (a-e) were suggested using lead molecule modification. Density functional theory (DFT) including MEP map and HOMO-LUMO analysis were used for the newly proposed compounds to predict the reactivity zones on the molecules, stability, and chemical reactivity. DFT calculation illustrated that these new compounds were stable. The estimated binding free energy (ΔG) values for a-e compounds were obtained as -5.78, -5.81, -5.95, -5,98, and -6.11 kcal/mol, respectively. Finally, the pharmaceutical properties and toxicity of these new compounds were estimated through OSIRIS DataWarrior software. The results indicated no risk of tumorigenic, irritant, or reproductive effects and mutagenicity for compounds d and e. As a result, compounds d and e, could be selected for further study as potential therapeutic candidates. Moreover, employing molecular docking simulation with the prediction of pharmaceutical properties helps to discover new potential drug compounds.

Keywords: drug design, anticancer, computational studies, DFT analysis

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Gadiri Sabiha

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Introduction: Current allergy diagnostic tools using Multiplex technology have made it possible to increase the efficiency of the search for specific IgE. This opportunity is provided by the newly developed “Alex Biochip”, consisting of a panel of 282 allergens in native and molecular form, a CCD inhibitor, and the potential for detecting cross-reactive allergens. We evaluated the performance of this technology in detecting cross-reactivity in previously explored patients. Material/Method: The sera of 39 patients presenting sensitization and polysensitization profiles were explored. The search for specific IgE is carried out by the Alex ® IgE Biochip, and the results are analyzed by nature and by molecular family of allergens using specific software. Results/Discussion: The analysis gave a particular profile of cross-reactivity allergens: 33% for the Ole e1 family, 31% for NPC2, 26% for storage proteins, 20% for Tropomyosin, 10% for LTPs, 10% for Arginine Kinase and 10% for Uteroglobin CCDs were absent in all patients. The “Ole e1” allergen is responsible for a pollen-pollen cross allergy. The storage proteins found and LTP are not species-specific, causing cross-pollen-food allergy. The nDer p2 of the NPC2 family is responsible for cross-reactivity between mite species. Conclusion: The cross-reactivities responsible for mixed syndromes at diagnosis in our patients were dominated by pollen-pollen and pollen-food syndromes. They allow the identification of severity factors linked to the prognosis and the best-adapted immunotherapy.

Keywords: specific IgE, allergy, cross reactivity, molecular allergens

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Authors: Temnov D., Volgina E., Gerasimov D.

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Relaxation processes in polyvinylidene fluoride (PVDF) films were studied by the method of thermally stimulated fractional polarization currents (TSTF). The films were obtained by extrusion of a polymer melt followed by isometric annealing. PVDF granules of the Kynar-720 brand (Atofina Chemicals, USA) with a molecular weight of Mw=190,000 g•mol-1 were used for the manufacture of films. The annealing temperature was varied in the range from 120 °C to 170 °C in increments of 10 °C. The dependences of the degree of crystallinity of films (χ) and the intensity of thermally stimulated depolarization currents on the annealing temperature (Toc) are investigated. The TSTF spectra were obtained at the TSC II facility (Setaram, France). Measurements were carried out in a helium atmosphere, and the values of currents were determined by a Keithley electrometer. The annealed PVDF films were polarized at an electric field strength of 100 V/mm at a temperature of 31°C, after which they were cooled to 26°C, at which they were kept for 1 minute. During depolarization, the external field was removed, and the short-circuit sample was cooled to 0°C. The thermally stimulated short-circuit current was recorded during linear heating. Relaxation processes in PVDF films were studied in the temperature range from 0 – 70 °C. It is shown that the intensity curve of the peaks of TST FP has a course that is the reverse of the dependence of the degree of crystallinity on the annealing temperature. This allows us to conclude that the relaxation processes occurring in PVDF in the 35°C region are associated with the amorphous part of the structure of PVDF films between the layers of the spherulite crystalline phase.

Keywords: molecular and supramolecular structure, thermally stimulated currents, polyvinylidene fluoride films, relaxation processes

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Authors: Amr A. EL Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir , Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed

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In the vicinity of the red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54 %) and Penicillium commune (48 %) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has the capability of degradation and can be utilized for cleaning the Saudi Arabian environment.

Keywords: fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS

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Authors: Amit Tribedi

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Genuine Quantumness present in Quantum Systems is the resource for implementing Quantum Information and Computation Protocols which can outperform the classical counterparts. These Quantumness measures encompass non-local ones known as quantum entanglement (QE) and quantum information theoretic (QIT) ones, e.g. Quantum Discord (QD). In this paper, some well-known measures of QE and QD in some wheel-like frustrated molecular magnetic systems have been studied. One of the systems has already been synthesized using coordination chemistry, and the other is hypothetical, where the dominant interaction is the spin-spin exchange interaction. Exact analytical methods and exact numerical diagonalization methods have been used. Some counter-intuitive non-trivial features, like non-monotonicity of quantum correlations with temperature, persistence of multipartite entanglement over bipartite ones etc. indicated by the behaviour of the correlations and the QIT measures have been found. The measures, being operational ones, can be used to realize the resource of Quantumness in experiments.

Keywords: 0D Magnets, discord, entanglement, frustration

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Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić, Stela Jokić

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The subject of this paper is to correlate antibacterial behavior of benzimidazole derivatives with their molecular characteristics using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on the inhibitory activity of benzimidazole derivatives against Staphylococcus aureus. The data were processed by linear least squares (LLS) and artificial neural network (ANN) procedures. The LLS mathematical models have been developed as a calibration models for prediction of the inhibitory activity. The quality of the models was validated by leave one out (LOO) technique and by using external data set. High agreement between experimental and predicted inhibitory acivities indicated the good quality of the derived models. These results are part of the CMST COST Action No. CM1306 "Understanding Movement and Mechanism in Molecular Machines".

Keywords: Antibacterial, benzimidazoles, chemometric, QSAR.

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Authors: Babak Safaei, A. M. Fattahi

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Polymer/carbon nanotube nanocomposites have a wide range of promising applications Due to their enhanced properties. In this work, free vibration analysis of single-walled carbon nanotube-reinforced composite plates is conducted in which carbon nanotubes are embedded in an amorphous polyethylene. The rule of mixture based on various types of plate model namely classical plate theory (CLPT), first-order shear deformation theory (FSDT), and higher-order shear deformation theory (HSDT) was employed to obtain fundamental frequencies of the nanocomposite plates. Generalized differential quadrature (GDQ) method was used to discretize the governing differential equations along with the simply supported and clamped boundary conditions. The material properties of the nanocomposite plates were evaluated using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites. Then the results obtained directly from MD simulations were fitted with those calculated by the rule of mixture to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results are presented to address the influences of nanotube volume fraction and edge supports on the value of fundamental frequency of carbon nanotube-reinforced composite plates corresponding to both long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, free vibration, generalized, differential quadrature (GDQ) method

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: S. Chandrasekaran, S. Nandita, M. Shivathmika, Srikrishnan Shivakumar

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The objective of the research work is to analyze the computational chemical-composition of carbohydrates in the context of healthcare informatics. The computation involves the representation of complex chemical molecular structure of carbohydrate using graph theory and in a deployable Chemical Markup Language (CML). The parallel molecular structure of the chemical molecules with or without other adulterants for the sake of business profit can be analyzed in terms of robustness and derivatization measures. The rural healthcare program should create awareness in malnutrition to reduce ill-effect of decomposition and help the consumers to know the level of such energy storage mixtures in a quantitative way. The earlier works were based on the empirical and wet data which can vary from time to time but cannot be made to reuse the results of mining. The work is carried out on the quantitative computational chemistry on carbohydrates to provide a safe and secure right to food act and its regulations.

Keywords: carbohydrates, chemical-composition, chemical markup, robustness, food safety

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Authors: S. Dargouthi, S. Boughdiri, B. Tangour

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This work invoked two complementary parts. In the first, we performed a theoretical study of various dimers of molecular of titanium dioxide. Five structures were examined. Three among them, the (T), (C) and (T/P) isomers, may be considered as stable compounds because they represent absolute minima on their potential energy surfaces. (T) and (C) may coexist because they are separted by only 6.5 kcal mol-1 but (T/P) dimer is in a metastable state from an energetic point of view. Non bonded dimer (P) transforms into its homologue (O) which has been considered as transitory specie with low lifetime which evolves to (T) structure. In the second part, we highlight the possible stabilization of (T), (C) and (P) dimers by encapsulation in carbon nanotubes. This indicates the probable role that plays this transitory specie the polymerization process of molecular TiO2. Confinement is suitable to control the fast evolution process and could towards the synthesis of new titanium dioxide nanostructured materials. An alternative description of TiO2 polymorphs (Rutie, anatase et Brookite) is proposed from (T), (C) and (T/P) dimmers motifs.

Keywords: titanium dioxide, carbon nanotube, confinement. encapsulation, transitory specie

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Authors: Eunjung Lee

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This research investigates the intricate connection between cultural differences and online consumer behaviors by integrating Hofstede's Cultural Dimensions theory with analysis methodologies such as text mining, data mining, and topic analysis. Our aim is to provide a comprehensive understanding of how national cultural differences influence individuals' behaviors when engaging with online reviews. To ensure the relevance of our investigation, we systematically analyze and interpret the cultural nuances influencing online consumer behaviors, especially in the context of online reviews. By anchoring our research in Hofstede's Cultural Dimensions theory, we seek to offer valuable insights for marketers to tailor their strategies based on the cultural preferences of diverse global consumer bases. In our methodology, we employ advanced text mining techniques to extract insights from a diverse range of online reviews gathered globally for a specific product or service like Netflix. This approach allows us to reveal hidden cultural cues in the language used by consumers from various backgrounds. Complementing text mining, data mining techniques are applied to extract meaningful patterns from online review datasets collected from different countries, aiming to unveil underlying structures and gain a deeper understanding of the impact of cultural differences on online consumer behaviors. The study also integrates topic analysis to identify recurring subjects, sentiments, and opinions within online reviews. Marketers can leverage these insights to inform the development of culturally sensitive strategies, enhance target audience segmentation, and refine messaging approaches aligned with cultural preferences. Anchored in Hofstede's Cultural Dimensions theory, our research employs sophisticated methodologies to delve into the intricate relationship between cultural differences and online consumer behaviors. Applied to specific cultural dimensions, such as individualism vs. collectivism, masculinity vs. femininity, uncertainty avoidance, and long-term vs. short-term orientation, the study uncovers nuanced insights. For example, in exploring individualism vs. collectivism, we examine how reviewers from individualistic cultures prioritize personal experiences while those from collectivistic cultures emphasize communal opinions. Similarly, within masculinity vs. femininity, we investigate whether distinct topics align with cultural notions, such as robust features in masculine cultures and user-friendliness in feminine cultures. Examining information-seeking behaviors under uncertainty avoidance reveals how cultures differ in seeking detailed information or providing succinct reviews based on their comfort with ambiguity. Additionally, in assessing long-term vs. short-term orientation, the research explores how cultural focus on enduring benefits or immediate gratification influences reviews. These concrete examples contribute to the theoretical enhancement of Hofstede's Cultural Dimensions theory, providing a detailed understanding of cultural impacts on online consumer behaviors. As online reviews become increasingly crucial in decision-making, this research not only contributes to the academic understanding of cultural influences but also proposes practical recommendations for enhancing online review systems. Marketers can leverage these findings to design targeted and culturally relevant strategies, ultimately enhancing their global marketing effectiveness and optimizing online review systems for maximum impact.

Keywords: comparative analysis, cultural dimensions, marketing intelligence, national culture, online consumer behavior, text mining

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Authors: Hiroyuki Aoki

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The glass transition phenomenon has been extensively studied for a long time. The glass transition of polymer materials is assigned to the transition of the dynamics of the chain backbone segment. However, the detailed mechanism of the transition behavior of the segmental motion is still unclear. In the current work, the single molecule detection technique was employed to reveal the trajectory of the molecular motion of the single polymer chain. The center segment of poly(butyl methacrylate) chain was labeled by a perylenediimide dye molecule and observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was analyzed near the glass transition temperature. The direct observation of the individual polymer chains revealed the intermittent behavior of the segmental motion, indicating the spatial inhomogeneity.

Keywords: glass transition, molecular motion, polymer materials, single molecule

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Authors: Albina V. Moskvicheva, Gevorg G. Kazarian, Anna R. Valeeva, Marina A. Efimova, Malik N. Mukminov, Eduard A. Shuralev, Rustam Kh. Ravilov, Kamil S. Khaertynov

Abstract:

Improving the early diagnosis of tuberculosis and solving a number of problems associated with the differential diagnosis of Mycobacterium bovis infection, nonspecific tuberculin reactions caused by sensitization of the body by non-tuberculosis mycobacteria, is urgent. The filtrates and extracts of M. bovis cell surface components are promising antigens with diagnostic potential. The purpose of this study was to isolate and characterize antigenic proteins and determine the dominant M. bovis antigens recognized by the humoral immune system. The mycobacterial cells were homogenized on FastPrep-24. Gel-filtration chromatography was used to fractionate the lysates of cell surface component extracts and proteins isolated from M. bovis culture supernatant. The separated fractions were analyzed using two-dimensional gel electrophoresis followed by determination of antigen serological activity using immunoblot with specific hyperimmune rabbit blood serum. As a result of electrophoretic separation of components by molecular weight, 23 antigen fractions were obtained. Analysis of densitograms showed that the fractions contained two zones of antigens with pronounced serological activity, corresponding to molecular weights of 28 and 21 kDa. The high serological activity of the 28 kDa antigen was established by immunoblot using hyperimmune blood sera. Separated and characterized by M. bovis specific antigen with a molecular weight of 28 kDa was added to the collection of specific marker antigens for M. bovis.

Keywords: antigen, gel-filtration chromatography, immunoblot, Mycobacterium bovis

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Authors: Javier Varillas, Jorge Alcalá

Abstract:

We investigate dislocation avalanche phenomena in face-centered cubic (FCC) and body-centered cubic (BCC) crystals using massive, large-scale molecular dynamics (MD) simulations. The analysis is focused on the intermittent development of dense dislocation arrangements subjected to uniaxial tensile straining under displacement control. We employ a novel computational scheme that allows us to inject an entangled dislocation structure in periodic MD domains. We assess the emission of plastic bursts (or dislocation avalanches) in terms of the sharp stress drops detected in the stress-strain curve. The plastic activity corresponds to the sporadic operation of specific dislocation glide processes exhibiting quiescent periods between successive avalanche events. We find that the plastic intermittences in our simulations do not overlap in time under sufficiently low strain rates as dissipation operates faster than driving, where the dense dislocation networks evolve through the emission of dislocation avalanche events whose carried slip adheres to self-organized power-law distributions. These findings enable the extension of the slip distributions obtained from strict displacement-controlled micropillar compression experiments towards smaller values of slip size. Our results furnish further understanding upon the development of entangled dislocation networks in metal plasticity, including specific mechanisms of dislocation propagation and annihilation, along with the evolution of specific dislocation populations through dislocation density analyses.

Keywords: dislocations, intermittent plasticity, molecular dynamics, slip distributions

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

Abstract:

Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

Abstract:

Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Siti Rafeah Md Rafei, Karen Wang Yanping, Park Mi Kyoung

Abstract:

Tissue samples are precious supply for molecular studies or disease identification diagnosed using molecular assays, namely real-time PCR (qPCR). It is critical to establish the most favorable nucleic acid extraction that gives the PCR-amplifiable genomic DNA. Furthermore, automated nucleic acid extraction is an appealing alternative to labor-intensive manual methods. Operational complexity, defined as the number of steps required to obtain an extracted sample, is one of the criteria in the comparison. Here we are comparing the One BioMed’s automated X8 platform with the commercially available manual-operated kits from QIAGEN Mini Kit and Roche. We extracted DNA from rat fresh-frozen tissue (from different type of organs) in the matrices. After tissue pre-treatment, it is added to the One BioMed’s X8 pre-filled cartridge, and the QIAGEN QIAmp column respectively. We found that the results after subjecting the eluates to the Real Time PCR using BIORAD CFX are comparable.

Keywords: DNA extraction, frozen tissue, PCR, qPCR, rat

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

Abstract:

Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Emad A. Mohammed

Abstract:

Utilizing the capabilities of Data Mining and Artificial Intelligence in the prediction of the minimum miscibility pressure (MMP) required for multi-contact miscible (MCM) displacement of reservoir petroleum by hydrocarbon gas flooding using Fuzzy Logic models and Artificial Neural Network models will help a lot in giving accurate results. The factors affecting the (MMP) as it is proved from the literature and from the dataset are as follows: XC2-6: Intermediate composition in the oil-containing C2-6, CO2 and H2S, in mole %, XC1: Amount of methane in the oil (%),T: Temperature (°C), MwC7+: Molecular weight of C7+ (g/mol), YC2+: Mole percent of C2+ composition in injected gas (%), MwC2+: Molecular weight of C2+ in injected gas. Fuzzy Logic and Neural Networks have been used widely in prediction and classification, with relatively high accuracy, in different fields of study. It is well known that the Fuzzy Inference system can handle uncertainty within the inputs such as in our case. The results of this work showed that our proposed models perform better with higher performance indices than other emprical correlations.

Keywords: MMP, gas flooding, artificial intelligence, correlation

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